[,codonTable-method {coRdon} | R Documentation |
Subset codonTable
object.
Description
Subset codonTable
object.
Usage
## S4 method for signature 'codonTable'
x[i]
## S4 method for signature 'codonTable'
x[[i]]
## S3 method for class 'codonTable'
subset(x, subset, ...)
Arguments
x |
A codonTable object to be subset.
|
i |
indices specifying elements to extract or replace. Indices are
numeric or character vectors or empty (missing) or
NULL . Numeric values are coerced to integer as by
as.integer (and hence truncated towards zero).
Character vectors will be matched to the names of the
object (or for matrices/arrays, the dimnames ):
see ‘Character indices’ below for further details.
For [ -indexing only: i , j , ... can be
logical vectors, indicating elements/slices to select. Such vectors
are recycled if necessary to match the corresponding extent.
i , j , ... can also be negative integers,
indicating elements/slices to leave out of the selection.
When indexing arrays by [ a single argument i can be a
matrix with as many columns as there are dimensions of x ; the
result is then a vector with elements corresponding to the sets of
indices in each row of i .
An index value of NULL is treated as if it were integer(0) .
|
subset |
A logical or character vector indicating which elements of
x to keep. If logical, subset should be of length
length(x) . If character, subset should contain
at least some of the elements of either getKO(x) or
getCOG(x) .
|
... |
further arguments to be passed to or from other methods.
|
Value
subsets of codonTable
object, keeping in each slot
only those elements that meet the criteria in subset
, if specified.
Examples
# create codonTable
mat <- matrix(sample(1:10, 610, replace = TRUE), nrow = 10)
cT <- codonTable(mat) # produces informative warning
cT
cT[1]
cT[[1]]
subset(cT, c(rep(c(TRUE,FALSE), 5))) # subset odd sequences
cT <- setKO(cT, rep(c("K00001", "K00002"), 5))
subset(cT, "K00001")
cT <- setCOG(cT, rep(c("COG0001", "COG0002"), 5))
subset(cT, "COG0001")
[Package
coRdon version 1.12.0
Index]